Rapid evolutionary dynamics of pepper mild mottle virus

Guan, Xiayu; Yang, Caixia; Fu, Jingjing; Ho, Simon Y. W.; Gao, Fangluan

doi:10.1016/j.virusres.2018.08.006

Cited by 8 publications

(4 citation statements)

References 35 publications

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“…It has been shown that all five genes encoded by ASPV had large genetic variability, especially in the CP-encoding ORF5. The CP gene is one of the most commonly used markers for evolutionary analyses of viruses in the Betaflexiviridae family [11][12][13] as well as for other plant viruses [14][15][16][17][18]. Previous studies about the genetic diversity of ASPV isolates have shown that the nucleotide identity among CP sequences was high, though with a certain degree of discrepancy among studies: between 81.7-99.3 % [4], 64.…”

Section: Introductionmentioning

confidence: 99%

Evolving by deleting: patterns of molecular evolution of Apple stem pitting virus isolates from Poland

Komorowska

Hasiów‐Jaroszewska

Elena

2019

Journal of General Virology

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In this study, 267 coat protein gene (CP) sequences from 48 Polish isolates of Apple stem pitting virus (ASPV) were determined. The genetic structure of the virus population was analysed and possible mechanisms of molecular evolution explored. We found evidence of recombination within the ASPV population and the presence of 17 ASPV molecular variants that differ in the length, number and arrangement of deletions in the CP. Population genetic analyses showed significant variation among isolates from pear and apple trees, between isolates from the same host species and, more interestingly, within isolates, supporting the existence of significant levels of variability within individual hosts, as expected by a quasispecies population structure. In addition, different tests support that selection might have been an important force driving diversification within isolates: positive selection was found acting upon certain amino acids. Phylogenetic analyses also showed that isolates did not classify according to the host species (pear or apple trees) but according to the pattern of deletions, suggesting a possible role for deletions during clade diversification.

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Section: Introductionmentioning

confidence: 99%

Evolving by deleting: patterns of molecular evolution of Apple stem pitting virus isolates from Poland

Komorowska

Hasiów‐Jaroszewska

Elena

2019

Journal of General Virology

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“…We initially used bell peppers as a source of PMMoV as this fruit has commonly been shown to contain PMMoV [ 20 ]. The presence of PMMoV may vary on the geographical source of peppers, but we selected peppers that showed evidence of mottling, associated with PMMoV infection.…”

Section: Discussionmentioning

confidence: 99%

Development and evaluation of TaqMan-based, one-step, real-time RT-PCR assays for pepper mild mottle virus detection for near source tracking and wastewater-based epidemiology validation

Cantillon

Roberts

2022

PLoS ONE

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Emergence of novel human pathogens pose significant challenges to human health as highlighted by the SARS-CoV-2 pandemic. Wastewater based epidemiology (WBE) has previously been employed to identify viral pathogens and outbreaks by testing samples from regional wastewater treatment plants. Near source tracking (NST) allows for more targeted WBE by analysing samples from individual buildings such as schools or even individual floors such as in multi-floor office buildings. Despite the public health advantages of WBE, few strategies exist for optimising NST sampling methodologies. Therefore, we developed a protocol to evaluate virus detection in NST sampling using Pepper Mild Mottle Virus (PMMoV) as a proxy for RNA viruses. PMMoV is the most abundant enteric human associated RNA virus and is present in peppers/pepper-containing foods. Two bespoke TaqMan RT-PCR assays were developed to detect a PMMoV genomic 5’ region and a capsid associated gene. To evaluate the protocol against field samples, pepper homogenates were flushed down an in-use toilet (Liverpool School of Tropical Medicine, UK) to spike wastewater with PMMoV on multiple days, and samples collected from two sewage access points to validate NST samplers. These wastewater samples were assessed for PMMoV based on Ct values and results compared to pepper and Tabasco derived PMMoV positive controls. Positive detection of PMMoV was comparable and consistent in ten independent samples across two NST samplers regardless of pepper homogenate spiking. We have developed two novel one step TaqMan assays that amplify both PMMoV targets in viral RNA extractions from peppers, Tabasco, and wastewater samples with cDNA synthesis through to RT-PCR results taking approximately 30 minutes. Pepper homogenate flushing was not required to detect PMMoV in our wastewater samples, however this strategy of flushing PMMoV containing materials outlined here could be valuable in assessing and validating NST in buildings with no previous or current sewage flow.

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“…Emerging of large numbers of pathogens is considered as a major constraint factor on crop losses, which adversely affects both crop yield and quality. Among them, pepper mild mottle virus (PMMoV), a typical member of the genus Tobamovirus , family Virgaviridae , has caused tremendous damage to crops due to extreme stablity in the environment and transmitting easily. − Subsequent studies have shown that PMMoV is associated with fever, itching, abdominal pain, and other clinical symptoms, revealing that it may pose a major threat to human health . Since the first discovery of Tobamovirus , unremitting efforts have been directed to control and eradicate it, including fumigation of soil with methyl bromide, screening of novel resistant genes, seed sterilization, breeding programs, and inoculation with attenuated viruses.…”

Section: Introductionmentioning

confidence: 99%

Inactivating Activities and Mechanism of Imidazo[1,2-c]pyrimidin-5(6H)-one Nucleoside Derivatives Incorporating a Sulfonamide Scaffold

Yang

Song

Yin

et al. 2023

J. Agric. Food Chem.

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Twenty-eight imidazo[1,2-c]pyrimidin-5(6H)-one nucleoside derivatives incorporating a sulfonamide scaffold with preferable inactivating activities on pepper mild mottle virus (PMMoV) were designed and synthesized. Then, compound B29 with illustrious inactivating activity against PMMoV was received on the basis of the three-dimensional quantitative structure–activity relationship (3D-QSAR) model, with the EC50 of 11.4 μg/mL, which was superior to ningnanmycin (65.8 μg/mL) and template molecule B16 (15.3 μg/mL). Furthermore, (1) transmission electron microscopy (TEM) indicated that B29 could cause severe fracture of virions; (2) microscale thermophoresis (MST) and molecular docking further demonstrated that B29 had faintish binding affinities with PMMoV CPR62A (K d = 202.84 μM), PMMoV CPL144A (K d = 141.57 μM), and PMMoV CPR62A,L144A (K d = 332.06 μM) compared to PMMoV CP (K d = 4.76 μM); and (3) western blot and reverse transcription-quantitative polymerase chain reaction (RT-qPCR) results of pCB-GFP-PMMoV CPR62A, pCB-GFP-PMMoV CPL144A, and pCB-GFP-PMMoV CPR62A,L144A were consistent with MST and confocal. In brief, the above results indicated that the amino acids at positions 62 and 144 of PMMoV CP might be the key amino acid sites of B29 acted on.

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Rapid evolutionary dynamics of pepper mild mottle virus

Cited by 8 publications

References 35 publications

Evolving by deleting: patterns of molecular evolution of Apple stem pitting virus isolates from Poland

Evolving by deleting: patterns of molecular evolution of Apple stem pitting virus isolates from Poland

Development and evaluation of TaqMan-based, one-step, real-time RT-PCR assays for pepper mild mottle virus detection for near source tracking and wastewater-based epidemiology validation

Inactivating Activities and Mechanism of Imidazo[1,2-c]pyrimidin-5(6H)-one Nucleoside Derivatives Incorporating a Sulfonamide Scaffold

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